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Load Xenium mask labels using Dask

Open marcovarrone opened this issue 2 months ago • 1 comments

Towards #228

Replace the code to load the Xenium segmentation masks to use Dask to greatly reduce the memory consumption of the Xenium reader.

I abandoned the idea of saving each element to free up memory because the Xenium reader is already mostly Dask-compatible, so it will not bring any advantage.

marcovarrone avatar Oct 28 '25 11:10 marcovarrone

Codecov Report

:x: Patch coverage is 0% with 1 line in your changes missing coverage. Please review. :white_check_mark: Project coverage is 37.81%. Comparing base (7cccdd1) to head (0c80218). :warning: Report is 27 commits behind head on main.

Files with missing lines Patch % Lines
src/spatialdata_io/readers/xenium.py 0.00% 1 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (7cccdd1) and HEAD (0c80218). Click for more details.

HEAD has 1 upload less than BASE
Flag BASE (7cccdd1) HEAD (0c80218)
3 2
Additional details and impacted files
@@             Coverage Diff             @@
##             main     #337       +/-   ##
===========================================
- Coverage   49.06%   37.81%   -11.26%     
===========================================
  Files          26       26               
  Lines        2686     2721       +35     
===========================================
- Hits         1318     1029      -289     
- Misses       1368     1692      +324     
Files with missing lines Coverage Δ
src/spatialdata_io/readers/xenium.py 19.11% <0.00%> (-53.53%) :arrow_down:

... and 5 files with indirect coverage changes

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codecov-commenter avatar Oct 28 '25 11:10 codecov-commenter